Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 09:00:10 -0400 (Wed, 17 Oct 2018).
Package 1038/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
ORFik 1.0.0 Kornel Labun
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK |
Package: ORFik |
Version: 1.0.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.0.0.tar.gz |
StartedAt: 2018-10-16 23:05:03 -0400 (Tue, 16 Oct 2018) |
EndedAt: 2018-10-16 23:10:35 -0400 (Tue, 16 Oct 2018) |
EllapsedTime: 331.7 seconds |
RetCode: 0 |
Status: OK |
CheckDir: ORFik.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/ORFik.Rcheck’ * using R version 3.5.1 Patched (2018-07-12 r74967) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘ORFik/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘ORFik’ version ‘1.0.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘ORFik’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... OK * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.7-bioc/meat/ORFik.Rcheck/00check.log’ for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’ * installing *source* package ‘ORFik’ ... ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c findORFsHelpers.cpp -o findORFsHelpers.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfs.cpp -o findOrfs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rcpp/include" -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.o clang++ -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/ORFik/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ORFik)
ORFik.Rcheck/tests/testthat.Rout
R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin15.6.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(ORFik) Loading required package: IRanges Loading required package: BiocGenerics Loading required package: parallel Attaching package: 'BiocGenerics' The following objects are masked from 'package:parallel': clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap, parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB The following objects are masked from 'package:stats': IQR, mad, sd, var, xtabs The following objects are masked from 'package:base': Filter, Find, Map, Position, Reduce, anyDuplicated, append, as.data.frame, basename, cbind, colMeans, colSums, colnames, dirname, do.call, duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit, which, which.max, which.min Loading required package: S4Vectors Loading required package: stats4 Attaching package: 'S4Vectors' The following object is masked from 'package:base': expand.grid Loading required package: GenomicRanges Loading required package: GenomeInfoDb Loading required package: GenomicAlignments Loading required package: SummarizedExperiment Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: DelayedArray Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Loading required package: BiocParallel Attaching package: 'DelayedArray' The following objects are masked from 'package:matrixStats': colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges The following objects are masked from 'package:base': aperm, apply Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:DelayedArray': type The following object is masked from 'package:base': strsplit Loading required package: Rsamtools > > test_check("ORFik") ══ testthat results ═══════════════════════════════════════════════════════════ OK: 222 SKIPPED: 0 FAILED: 0 > > proc.time() user system elapsed 50.359 1.697 48.316
ORFik.Rcheck/ORFik-Ex.timings
name | user | system | elapsed | |
computeFeatures | 0.003 | 0.000 | 0.003 | |
computeFeaturesCage | 0.005 | 0.000 | 0.005 | |
coverageByWindow | 0.743 | 0.051 | 0.799 | |
coveragePerTiling | 0.320 | 0.046 | 0.369 | |
defineTrailer | 0.189 | 0.028 | 0.219 | |
detectRibosomeShifts | 0.002 | 0.001 | 0.003 | |
disengagementScore | 0.468 | 0.037 | 0.508 | |
distToCds | 0.372 | 0.002 | 0.382 | |
entropy | 1.002 | 0.004 | 1.013 | |
extendLeaders | 0.788 | 0.011 | 0.815 | |
findMapORFs | 0.725 | 0.002 | 0.731 | |
findORFs | 0.052 | 0.001 | 0.052 | |
findORFsFasta | 0.019 | 0.001 | 0.020 | |
firstEndPerGroup | 0.087 | 0.000 | 0.088 | |
firstExonPerGroup | 0.076 | 0.000 | 0.076 | |
firstStartPerGroup | 0.064 | 0.000 | 0.065 | |
floss | 0.164 | 0.001 | 0.165 | |
fpkm | 0.065 | 0.000 | 0.065 | |
fractionLength | 0.066 | 0.000 | 0.067 | |
fread.bed | 0.048 | 0.009 | 0.059 | |
getStartStopWindows | 4.592 | 0.342 | 3.886 | |
groupGRangesBy | 0.044 | 0.001 | 0.046 | |
insideOutsideORF | 0.786 | 0.002 | 0.792 | |
isInFrame | 0.334 | 0.001 | 0.340 | |
isOverlapping | 0.277 | 0.001 | 0.282 | |
kozakSequenceScore | 0.455 | 0.001 | 0.467 | |
lastExonEndPerGroup | 0.086 | 0.000 | 0.088 | |
lastExonPerGroup | 0.080 | 0.000 | 0.081 | |
lastExonStartPerGroup | 0.078 | 0.000 | 0.080 | |
makeORFNames | 0.111 | 0.001 | 0.112 | |
metaWindow | 0.203 | 0.003 | 0.206 | |
numExonsPerGroup | 0.081 | 0.000 | 0.083 | |
orfScore | 2.158 | 0.391 | 0.805 | |
rankOrder | 0.258 | 0.085 | 0.104 | |
reassignTSSbyCage | 0.363 | 0.002 | 0.372 | |
reduceKeepAttr | 0.249 | 0.001 | 0.251 | |
ribosomeReleaseScore | 0.226 | 0.001 | 0.228 | |
ribosomeStallingScore | 0.351 | 0.001 | 0.355 | |
seqnamesPerGroup | 0.089 | 0.001 | 0.092 | |
shiftFootprints | 0.001 | 0.000 | 0.002 | |
sortPerGroup | 0.328 | 0.001 | 0.335 | |
startCodons | 0.625 | 0.002 | 0.629 | |
startDefinition | 0.002 | 0.000 | 0.002 | |
startSites | 0.419 | 0.000 | 0.423 | |
stopCodons | 0.612 | 0.001 | 0.621 | |
stopDefinition | 0.002 | 0.001 | 0.002 | |
stopSites | 0.410 | 0.001 | 0.412 | |
strandBool | 0.013 | 0.000 | 0.013 | |
strandPerGroup | 0.101 | 0.000 | 0.102 | |
tile1 | 0.258 | 0.002 | 0.262 | |
translationalEff | 0.153 | 0.000 | 0.155 | |
txNames | 0.047 | 0.000 | 0.048 | |
txNamesWithLeaders | 1.196 | 0.009 | 1.203 | |
uniqueGroups | 0.552 | 0.345 | 0.209 | |
uniqueOrder | 0.363 | 0.001 | 0.372 | |
unlistGrl | 0.050 | 0.001 | 0.052 | |
widthPerGroup | 0.06 | 0.00 | 0.06 | |